Time Lord Fugue
by elrond peredhel
Summary: The Doctor finds his way back to Rose, but she doesn't want him anymore. Mysterious things happen upon his return to his universe. Set after Journey's End. Rated K for mild swearing in Chapter Two "Return" and Chapter Three "Renewal" .
1. Reunion

**Time Lord Fugue**

**Chapter one- Reunion**

"Rose."

The woman in question stopped dead in her tracks, her head whipping up in shock to gaze at the man sheepishly sat on the chair before her.

"John?" She screeched. "What are you doing in here? I've been through this so many times now, it's bad luck for the groom to see the bride before the wedding!"

"I think I know the traditions of a wedding Rose."

"So why are you here? Out! Now!" She pulled him to his feet and physically dragged him to the door. Confusion flickered briefly over the man's face, swiftly replaced by dawning realisation and then pain. He put up his hands in an attempt to get her to be quiet so he could explain himself; but, as with all Tyler women (in his view anyway), it is incredibly difficult to make them shut up.

"Rose!" He cried, trying to make himself heard over her ranting.

"Don't 'Rose' me mister. If this whole thing goes base-over-apex because of this... I swear, I swear, I don't know what I'll do!"  
His protests fell on deaf ears as the door swung open. Unable to see how else he could get Rose to listen to him, he grabbed her wrists and pressed her palms flat against his chest. She could feel the gentle thud of two heartbeats. Two hearts.  
Rose froze and stopped trying to throw him from the room.

"Rose, it's me," he said simply, placing his hands over hers. She stopped ranting.

"D...Doctor?" Rose squinted at his face, so familiar and yet so different, older even. "But it can't be... You said this world was sealed off properly this time- returning is impossible." A sad smile crossed the Doctor's lean, angular features.

"I know but, well..." he paused to sigh, "Jack managed to convert his Rift Manipulator and ta dah! Here I am." The chocolate brown eyes peered at her face, silently hoping she would believe. Rose stared at him a moment longer, struggling with a tide of emotions, before her face crumpled. She sobbed and launched herself at him, throwing her arms around his neck and relishing the feel of strong arms holding her tight, the distinctive sandal wood- and- universe scent that said ' The Doctor', a soothing aroma, his quiet voice a balm to her ragged soul.

"I missed you so much," she sobbed,

"I know." Abruptly she wrenched herself from their embrace.

"But you have to go. Now." Seeing his puzzled look, she clarified with a bitter laugh and shake of her head: "this isn't supposed to be possible, you said yourself, the worlds aren't stable enough for universe hopping any more. And now I'm marrying John-'' she sped on, stopping his question "the other you- it isn't fair on us if I'm constantly waiting for you to turn up. I'm happy here Doctor. I have a life, a job and I'm about to marry the man I love most, I... I just can't do this anymore. Living the double life, it's too much now. And I know you understand Doctor, it's the reason you always kept some sort of distance between us. You can't do everything to stop a relationship, and then change your mind now I'm with someone else."

Rose had to battle hard, not only to keep her voice steady, but to prevent herself from bursting into tears at the sight of the doctor's lost, hurt, forlorn expression. He closed his eyes slowly, wincing and swallowing convulsively as he turned his head away from Rose. After a few moments the doctor looked back at her, who flinched at the haunted pain and sorrow in his usually sparking- with- life eyes.

"Right. I'll just, go then." He managed to choke out before mentally shaking himself. "Goodbye Rose Tyler. Have a fantastic life." He added, in complete sincerity, looking from the floor to her eyes, a replay of the emergency programme he had previously recorded when he believed he would never see her again. "And rose? I... I lo..." She placed a finger softly on his lips ensuring that once again, he wouldn't get to finish his sentence.

"I know, Doctor." She whispered, before removing her finger and replacing it briefly, chastely with her lips in a kiss meant to last them forever. As she retreated, realisation broke on them both simultaneously and a single, glistening tear made its lonely trail down his left cheek as his eyes begged her to reconsider, already knowing she wouldn't. "Goodbye, my Doctor." She murmured as she followed his dejected form shuffling over to the door that hid his TARDIS. "I will always love you."


	2. Return

**Time Lord Fugue**

**Chapter two- Return**

Captain Jack Harkness sat comfortably in his office, leaning back in his leather chair, his booted feet propped up on the large, wooden corner desk in front of him. Things seemed to be going well lately; despite losing Tosh and Owen, he and the rest of Torchwood 3 had defended against a Dalek invasion of earth and then helped to return the stolen planet to its rightful place in the solar system. The weevils, it seemed, had been pretty put out by the whole event and opted to stay in the sewers. Perfect.

"Jack?" Ianto called his boss down to the various observation monitors located in his area of the Hub. "TARDIS materialising in Roald Dahl Plass now."

"I thought he wasn't coming back here?" Questioned Gwen, who had just returned from the extensive archives and only caught the tail end of the conversation by chance.

"So did I Gwen, so did I," came the usual enigmatic reply, the typically confident American drawl betraying his confusion. "I'll go topside and see what's up." Jack crossed the floor of the Hub and was about to reach the perception filtered elevator that would raise him up, side by side with the massive shining chrome water feature from the dark, damp bottom of the old Victorian railway station to the surface of the modern, 21st century Docks in Cardiff Bay when Ianto called out;

"Wait, Jack, he's disappeared. I can't find him on any of the scanners or cameras!"

"Shit! Where the Hell'd he go? Find him Ianto!" yelled Jack as he legged it back across the floor of the Hub and grabbed the faded blue cotton greatcoat and Webley revolver from his office. "I'm going after him. You two stay put. And I mean it this time Gwen! There's no knowing what might have happened out there, and I need to know you guys are safe." He fixed his Bluetooth headset onto his right ear and in three strides had lunged out the back door, ignoring the rest of the team's protests as he collided with the doctor. "Whoa! Watch where you're… Doctor?" Jack gazed in confusion at the figure sprawled over the floor in front of him. The Doctor shook his head and used the make-shift Tourist Information desk in the small room to haul himself back to his feet. "So, how'd it go? I know you weren't planning on coming back…" Jack's companionable prose drifted to a halt as the Doctor's eyes met his, tears streaming uncontrollably down his cheeks.

"I didn't tell her." He stated matter-of-factly "And before you say anything, of course I tried! It wasn't as if I just bottled it and came straight back!" Catching Jack's disbelieving look, he shoved past, into the Hub. Jack strode after his friend and grabbed his arm;

"I only asked a question, there's no need to get angry with me." He growled, barely holding his own temper in check now. The Doctor pulled away, shoving Jack into Tosh's newly unoccupied workstation, scattering piles of priceless and now useless tech.

"Of course there's something to be angry about!" The Doctor yelled, ignoring the startled looks of Ianto and Gwen whilst focusing his full 'Oncoming Storm' glare at Jack. "She told me to go Jack. She said she never wanted to see me again, and to prove it, she's marrying the other me. Hel, she even stopped me finishing my sentence! Now do you believe me?" All anger drained away in an instant, the Doctor once more became a sad, lonely child; looking to jack for assurance that he'd done the right thing by coming back. He sat heavily on the steps to the side of the wrecked work station, head in hands as the full enormity of Rose's words sunk in.

Jack stood and brushed his trousers down, motioning the two gawping Torchwood employees should leave the Hub.

"Come on, you need to rest Doc'," he murmured. He gently took the Doctor's arm and led him in the direction of the small room that acted as Jack's 'nap-zone' or bedroom on his all too frequent 24 hour shifts. While they walked he couldn't help but think that they'd have got at least a wolf-whistle from Owen by now, but before he could be completely lost in the past Gwen took Owens' role and changed a would be snide comment into a joke, no doubt trying to lighten the mood.

"He won't get much rest if you take him in there, Jack!" She grinned, before taking the frosty glare as a hint and retreating after Ianto.

"Here. It's not much, but its quiet here- you won't be disturbed." Jack told the Doctor, leading him to the small bed beneath the old, arched Victorian brickwork.

"Thank you Jack" came the simple reply as the Doctor tiredly eased his converses and pinstripe jacket off before slipping gratefully under the covers and pulling them up to his chin. As Jack made to leave, the Doctor reached out a slender hand from under the duvet; "stay, please? Until I fall asleep?"

'He has gorgeous eyes…' thought Jack as he gazed at the seemingly young man in his bed. He quickly shook himself; 'Damn it Jack Harkness! He needs your help, not advances!' and sat on the edge of the bed. "Course I will." A slow smile of thanks spread across the Doctor's face before his eyes drifted shut and a few minutes later his breathing deepened as sleep finally claimed the exhausted Time Lord.


	3. Renewal

**Time lord Fugue**

**Chapter 3 – Renewal**

The radio had barely declared it 6am when Jack returned to the Hub. He had only left a few hours ago, at the command of both Gwen and Ianto, but knowing The Doctor was then alone and therefore vulnerable had kept him awake. He dropped Ianto off at their apartment and feigned the need for a walk to clear his head in order to run back to Cardiff Bay to check on The Doctor.

Somehow Gwen beat him to it though, and was already sat on the dilapidated sofa, a mug of coffee in her hands and another steaming in wait on the low glass table in front of it.

"Hey Jack, I though you were staying here tonight?" She asked as he collapsed next to her and reached gratefully for the proffered mug of black coffee.

"Well I was, until you guys turfed me out." He sipped his piping hot drink and glanced sideways at Gwen, glimpsing her raised eyebrow before she managed to school her face to neutrality. "Ok, what?" he asked, placing his mug back on the table and shifting to face her, one arm draped casually over the back of the sofa, the other resting in his lap. Gwen shook her head and shrugged.

"I just wandered why you turfed out the dishy one for Big-Ears in there," she nodded her head towards The Doctor's room, "I mean, the ears are kind of cute, but he's a bit older than your usual type isn't he?" Jack looked at her as though she were drunk.

"What are you talking about Gwen? I haven't turfed anyone out;" he paused as her reference to Big-Ears sunk in. "Wait, older, with big ears?"

"Yeah, and a nose to go with 'em too!" As Jack's eyes widened in confused shock, he was already leaping up from the sofa and charging into his room to find that Gwen had been right: The Doctor was gone, replaced by another, more familiar face.

The man now in the bed, curled up in a protective foetal position under the covers was definitely older than the other man; in his early forties, sporting closely cropped mid-brown hair and impressively sized ears and nose that, in sleep, lent him an almost child-like appearance. The deep set lines etched into his brow revealed many worries and cares, but to Jack they seemed less prominent than they were the last time they had met, under fire from Daleks on Satellite 5. Jack gazed at the prone figure in awe. Regeneration was supposed to be irreversible, but here was The Doctor, _his_ Doctor; alive, well and asleep in the Torchwood Hub.

As though knowing he was under scrutiny, The doctor's brow furrowed as his eyes fluttered open, revealing a bleary dash of brilliant, icy blue. He frowned at Jack, who could almost see his mind working out where he was and what he was doing in bed with Jack Harkness, Captain of the Innuendo Squad, watching. Jack also saw him give up trying and resigning himself to the humility of asking- an action only ever to be fallen back on if his head was completely screwed.

"Jack, what's going on, where am I?" he mumbled, propping himself up on one elbow.

"You're in the Hub. Home of Torchwood Three; that's me, Gwen Cooper and Ianto Jones."

"Ok, so where exactly is the Hub? Doesn't look anything like Satellite 5 to me, an' I could swear that's where I left you. Plus, she's Human." The Doctor added, a tip of the head indicating Gwen, who stood in the corner of the room, quietly observing the two men.

"Oi! You say that like it's a bad thing!" She growled, taking a step forward. Jack put his arm out in her way and gave her 'The Look', stopping her from making any more rash moves.

"Abad thing? No!" The Doctor cried, leaping up from the bed. "You humans are fantastic! So tiny and new, but look at you; guarding the Rift, protecting Earth from alien threats and invasions- if I had to choose my favourite species in the universe, I would choose humans!"

Gwen screamed.

"Whoah, ok..." stuttered Jack, eyes wide at the sight of a 100% naked Doctor. "Gwen. My office. Second cabinet on the right, third drawer down. Get the jeans and jumper, oh and the jacket hung inside the door." He ordered, hustling the Doctor back under the covers. A few minutes later, a sleep ruffled Ianto poked his head round the door.

"Sorry if I'm interrupting anything, but Gwen asked me to bring you these Sir. He handed Jack a pile of neatly folded clothes.

"Cheers Ianto." Said Jack, handing the pile to The Doctor, who gratefully pulled them on.

"Will that be all, or do you want me to start the coffee?" At The Doctor's grimace Ianto added, "I'm sure I could find some tea, if you'd prefer?" Immediately The Doctor cheered up.

"White, no sugar thanks." He stated, a happy grin directed at Ianto. He turned back to Jack as Ianto left, no doubt to fix a coffee for himself, having only just arrived because of an urgent call from Gwen. "Right, clothes. Start talking." Commanded The Doctor. Jack shuffled his feet, a tad embarrassed.

"Well, I managed to use my Vortex Manipulator-'' The Doctor snorted derisively,

"Space Hopper."

"My Vortex Manipulator," Jack continued, more forcefully, "to get back to the 21st century, my clothes were kinda wrecked and out—dated, so I needed some new ones. Obviously I had no cash, and the only people I knew were you, Rose and Mickey; so I waited for the right version of you to stop in Cardiff to refuel the TARDIS. Once you left it to go look around while she charged, I used my key to sneak on board and grab some clothes. It just so happened that the TARDIS decided to give me a spare set of yours."

Gwen beckoned Ianto over to the CCTV screen set up to monitor Jack's room. Despite the walls being virtually sound proof, and the room only having a one-way mic', they couldn't help but instinctively whisper.

"I'm pretty sure we shouldn't be watching this." Hissed Ianto,

"Well tough. Jack's been keeping secrets Ianto, and I want to know why. I think that man," she pointed at the screen, "this 'Doctor' holds the key to those secrets. Who knows, we might even find out why Jack disappeared a few months ago."

"I still don't think we have the right to spy on him like this." He countered. "Whatever is going on in there, Jack probably wants it kept private, between The Doctor and himself." He glared at Gwen and reached over to terminate the video feed. Gwen grabbed his hand;

"You're only saying that 'cos you're shagging him!" She scoffed

"I am not!" Ianto squeaked in indignation.

"Oh, so he shags you then?" Gwen sneered, good naturedly.

"No! Well, yes." He hurried on, "but that's not the point! You were livid when Rhys found out about you working for Torchwood. It was your one little bit of privacy in your relationship- the one thing you didn't have to share, until he found out. How do you think Jack's going to react when he finds out we spied on him?" Ianto retorted angrily.

"That was different, I didn't tell him about Torchwood so I could keep him safe, what you don't know can't hurt you, and anyway, once he found out, I told him everything. We just found out about The Doctor and all Jack can do is moon over him and ignore us. Of course I want to know what's so damned special about him that Jack disappears without warning for months and then comes back just as suddenly with no word as to where he's been!"

Unaware of the argument raging in the main area of the hub, Jack and his enigmatic mystery guest were talking...


	4. Refuge

**Time Lord Fugue**

**Chapter Four- Refuge**

"Out-dated? You bought those clothes in the 21st Century!"

"Yeah I know, but I didn't actually manage to get straight here. I had to live through the Victorian era while I waited for the teleport to recharge- hence the out-dated clothes- and even then the closest I got was World War One. I lived and died through both the wars, got turned into one of those Gas Mask Zombies whilst trying to evade you guys and finally ended up in London around the right time to watch Rose grow up. After Canary Wharf, I decided something had to be done, so I started up Torchwood 3 here in Cardiff using my connections to the original torchwood from the 1800's." Jack looked across to The Doctor. "You do remember all this, right? I told you when we met at the end of the universe."

The Doctor looked puzzled and Jack sighed, "Ok, so what's the most recent thing you remember, other than being here and now?" The Doctor's brow furrowed as he closed his eyes, lips pursed in concentration.

"I remember Canary Wharf and Rose being in Pete's World. I blew up a sun just so I could say goodbye to her- we were at Darlig Ulv Stranden and she told me," he swallowed, "she loved me." His eyes opened and he looked at Jack tearfully. "I'm missing so much. I know there's other stuff that happened between then and now, but it's like a whacking great padlock has been stuck in my mind and I can't find the key…" Jack looked at the older man sympathetically,

"I know the feeling," he said with a grimace," from the sound of it, you're missing about two linear years' worth of memories- between the time you lost Rose, to yesterday when you found her again."

"Two years?" The doctor cried, alarmed at the full extent of his amnesia. "How can I lose two years?" He grabbed jack by the shoulders and shook him slightly as he lost control and began to really panic.

"Well, after Canary Wharf - and I know this 'cause you told me- you kinda went on a semi-suicidal rampage. You met a woman called Donna Noble and sorted out the Empress of the Racnoss at Christmas by setting her on fire and drowning her kids under the Thames." He held up a hand to stop The Doctor's question, "here's the suicidal bit. Instead of getting the Hell out of there while you still could, you decided to stay put. The only reason you weren't drowned or ripped apart past your regeneration capabilities was that Donna told you to stop. You went on to meet Martha Jones in a hospital on the Moon. She spent a year helping you get rid of The Master while we were his prisoners." At the mention of his old friend and enemy, The Doctor jerked forward.

"The Master? How could I meet him? I'm the only Time Lord left- the rest died in the Time War! Even if he was in a parallel universe I'd be able to sense him up here." He tapped his temple. "There's no one."

"Not anymore, no, but he was still alive. He turned himself into a human and hid at the end of the universe, until we found him, blew his cover and he made it to Prime Minister of Great Britain. We stopped him, but his wife shot him and he died in your arms, refusing to regenerate." He continued to describe the year that followed, from Donna's sacrifice in a parallel world made by changing a decision, to his Human-Time Lord Metacrisis resulting from his brush with a Dalek bolt and finally the destruction of Davros. Once he had finished his tale, Jack sat back and licked his dry lips as he waited for The Doctor to process the information.

Needing a drink, Jack bade The Doctor follow him out of the room. They walked in companionable silence until they reached the main Hub, where Jack strode over to the abandoned coffee machine to fix the drinks Ianto had promised and for some reason, forgotten. As he did this, The Doctor wandered over to the nearest work station where Gwen and Ianto were frantically trying to turn off the video feed before he discovered that they had been spying on the pair. Several photo's were knocked over and delicate models destroyed before they managed to get as far as turning the monitor off to hide the image of Jack's room that was plastered across the screen.

"Enjoy our little nosey did we?" The Doctor asked sweetly, eyebrows raised as he looked down his long nose at them. They both squirmed like schoolchildren caught pulling a prank on their teacher, but whereas Gwen hardened her face into an unreadable mask; Ianto broke under the stern, cold gaze easily.

"I'm sorry Sir! I did tell Gwen we shouldn't watch, ad it was breaching your privacy, but she wouldn't listen." He trailed off as The Doctor's jaw clenched, his eyes growing grey with anger.

"So you decided to watch anyway? To make sure _she_," he glowered at Gwen, who was now visibly shaking under his scrutiny, "didn't see anything useful, or did you not want to miss out on the action?" he finished, voice raised to almost a shout now. As he took a menacing step forward, Jack scrambled over and gripped his arm.

"Leave it Doc'." He growled. "We just lost two members of the team, and you picking a fight with the others is not going to help!" The Doctor sighed heavily and looked away. Apologetically he held out his hand to first Gwen and then Ianto;

"Friends?"

"Friends." They answered, taking his hand and gripping it in a shake. Silently they marvelled at the rough, calloused fingers and palm- he looked a bit of a brute on the outside, but from what they had seen and heard, he hadn't been wielding a sword regularly. The Doctor raised an eyebrow, amused when Ianto took longer than necessary to release his hand.

With an abrupt clap of his hands, The Doctor span around. His eyes lit up at the sight of Owen's medical bay-come- autopsy room and he vaulted easily over the railings to land comfortably beside the long table occupying the middle of the room.

"Right then, lets get this sorted out!" He rubbed his hands together in glee as Jack led the other two in a more sedate fashion down the stairs to see The Doctor eagerly riffling through drawers and cupboards with the enthusiasm of a magpie in a dragon's hoard. As the team joined him on the same level, he looked up and grinned his most manic grin.

"What exactly are we sorting out?" Queried Ianto, finding his arms full of a tangled bundle of cables and equipment. As The Doctor crouched to fiddle with the settings of Owen's computer, he half turned to face them,

"Gwen. You saw me last night and you say I look different now, yeah?" She nodded the affirmative. "And Jack, you know the me you saw last night is the man I will become when I regenerate next?" Well that implies that there's either two different versions of me running around Cardiff at the same time, which I know isn't possible 'cause I'd sense the other one, or somehow I degenerated back to this body from the newer one. That is impossible, so we need to find out how I'm here."

Taking stock of the equipment he had loaded onto Gwen and Ianto, he told them to dump it all and help him set up some tests. Setting the computer to reboot and install some clever new medical software, he hopped onto the examining table, pulling off his battered leather jacket and maroon v-neck jumper to allow Gwen to stick sensors at strategic places on his body: his temples, the insides of hid biceps, and over both hearts. As Ianto helped connect the attached wires to the pc, Jack took hold of The Doctor's right arm and deftly slid a needle and catheter into the vein inside his elbow. The doctor flinched and glared, the machine next to him emitting a loud beep to announce his pain. Quickly securing the offending instrument to his friend's arm, Jack added a blood bag which quickly began to fill with a deep reddy-blue liquid. The Doctor frowned slightly as he watched. "S' not supposed to be that blue…" he murmured before looking to check the rest of the machines were doing their jobs.

An hour later, fully clothed again, The Doctor wandered around the Hub with the results of his tests. Everything seemed to be normal, but he was still waiting for Jack to finish mucking about with the blood sample.

"Uh, Doc? I think I've got something." The Doctor ceased pacing and strode over to use the microscope Jack had just vacated for him. "See? I know you said your DNA was clever, but there is no way it should be changing that quickly! I mean, your cells are practically imploding." The younger man studied his friend. "What's going on?"

"No idea, though when you say imploding… That seems to ring a bell for some reason." He pinched the bridge of his nose between two long, slender fingers and closed his eyes to think. "Why did I come back?"

"Well Rose is marrying," Jack didn't get to finish his sentence as The Doctor clicked fingers,

"Oh you stupid, soppy fool, that's it!" he looked at Jack, "Fugue State." As his hand flew over his head in imitation of his understanding, Ianto chipped in to help his boss,

"Fugue State, it's a way of the mind dealing with extreme trauma- it sort of shuts down and blanks out the bad bits, creating a new persona to fill in the gaps."

"Exactly!" The Doctor nodded, "except because I'm a Time Lord, my version is a bit more physiological than that. Instead of just blocking bad memories, it forces me back to a previous body, one probably more suited to cope with the effects of rediscovering the memories that were hidden. I finally accept that Rose loves me, and that I really do feel the same way, I manage to get back to her again, despite telling them all it was definitely impossible this time and then she tells me she's marrying the half human me and that she never wants to see me again…"

"No offence, but having Rose move on with her life is kinda insignificant compared to the Time War. How come this Fugue happened now and not after that?" The Doctor nodded in acquiescence.

"As a whole, the Time War _is_ more important, much more traumatising, but I suppose it comes down to morals. I can deny that Rose has moved on for as long as I like, the only person going to get hurt is me, but to murder my own people and destroy my planet is one thing; to forget the victims of such genocide is even more unforgivable. I destroyed them Jack, and as I'm the only one left to deal with it, it is both my punishment and duty to see that their memories and knowledge live on- I can never forget what I did."


End file.
